When you run smbd -V on your Snow Leopard installation, you'll see it's running SAMBA version 3.0.28a-apple. While I'm not sure how much difference the "-apple" makes, version 3.0.28a is old. Very old. In other words, it's riddled with bugs. Apple hasn't updated SAMBA in 3 years, and for Lion, they're dumping it altogether for something homegrown. The reason? SAMBA is now GPLv3.

[...] For instance, if you put a Mac to sleep during a backup, it'll lock up because Netatalk doesn't support Replay Cache.

Thanks anyway for your help.

As steted previously, I suspect this issue is fixed from v. 2.2, which is currently in beta release.

The issue with Finder's Sidebar is only an issue with Kerberos based single sign-on, due to Apple's implementation of Finder's Sidebar.

On Debian and Ubuntu (at least), Netatalk supports DHX and DHX2 password schemes which allows for single sign-on if you save your password in a hidden file in your home directory on the server.

I've never myself used PAM with Netatalk and I've grown to hate Apple's Bonjour notoriously (mainly due to these little oddities Apple tends to introduce every now and them to distance themselves from standards just enough to be incompatible (did anyone say Microsoft??)) so I might not be able to help you with that, as much as I'd wish!